open2c/cooltools

Issues

• IndexError: index 0 is out of bounds for axis 0 with size 0

  #542 opened 21 days ago by shRDJr
  0

• problem generating visulazation with KR normalization

  #471 opened 9 months ago by jiangshan529
  3

• dist_bp and contact_frequency fields missing from CVD function.

  #512 opened 7 months ago by ratheraarif
  10

• Error when running cooltools random-sample

  #541 opened a month ago by GMFranceschini
  4

• Pool decorator doesn't allow 3rd party multiprocessing map functors

  #535 opened a month ago by dmitrymyl
  0

• Control/Observed whole genome.

  #537 opened 3 months ago by rkash
  1

• Issue with scoring_and_histogramming_step: ValueError: There are la_exp.donut.value in (8192.0, inf], please check the histogram

  #511 opened 2 months ago by satvikgunjala
  4

• Unable to install cooltools

  #524 opened 2 months ago by yuri-practice-only
  2

• how to get expected contact frequency

  #530 opened 2 months ago by BenxiaHu
  1

• Issue with pileup example

  #525 opened 2 months ago by erika-anderson
  1

• Can not install cooltools

  #538 opened 2 months ago by xiasijian
  1

• Performance of obs/exp pileups is significantly lower than of obs pileups with nproc > 1

  #536 opened 3 months ago by dmitrymyl
  0

• `Matplotlib` 3.9 broken dependency

  #520 opened 4 months ago by nvaulin
  3

• IndexError: Positional Indexers are Out-of-Bounds in Insulation Calculation

  #529 opened 4 months ago by g1g122
  3

• cooltools.eigs_cis encountered an error

  #528 opened 4 months ago by LHXqwq
  0

• mcool format conversion

  #527 opened 4 months ago by mdozmorov
  4

• update cooltools in conda

  #526 opened 5 months ago by fys666
  0

• Possible bug in insulation?

  #523 opened 5 months ago by gdolsten
  3

• cooltools insulation IndexError: positional indexers are out-of-bounds

  #522 opened 6 months ago by WenjuSun
  4

• Cooltools Dots problem in chicken genome with external mcool file

  #521 opened 6 months ago by pollicipes
  1

• cooltools virtual4c

  #519 opened 6 months ago by BenxiaHu
  4

• cooltools.virtual4c does not write valid .bw files

  #498 opened 10 months ago by StrohD
  2

• pileup around centromeres

  #491 opened 10 months ago by ratheraarif
  16

• cooltools.expected_cis output does not have the 'dist_bp' column

  #518 opened 7 months ago by danobaji
  2

• adaptive coarsegrain returns numpy attribute error

  #504 opened 7 months ago by danobaji
  0

• saddle plot

  #514 opened 7 months ago by BERICP01
  1

• first diagonal NaNs for smoothed expected_cis

  #509 opened 9 months ago by gfudenberg
  0

• fetch genomic feature issue when trying dots & focal enrichment

  #495 opened 9 months ago by yingsun-ucsd
  36

• cooltools.expected_cis(clr_weight_name = None) returns error asking for balanced data: smoothing breaks without a balanced column

  #456 opened 9 months ago by ddepierre
  3

• migrate log-smoothing to mini-library

  #505 opened 9 months ago by gfudenberg
  2

• cooltools.dots runs under different conda environments

  #508 opened 9 months ago by Jiangyuan-Liu
  2

• allow alternate reductions for aggregation across diagonals

  #507 opened 9 months ago by gfudenberg
  0

• synchronize CLI and API defaults for get_expected_cis smoothing & aggregation

  #506 opened 9 months ago by gfudenberg
  0

• insulation & edge effects: consider masking?

  #503 opened 9 months ago by gfudenberg
  0

• Issue with cooltools.api.snipping.pileup() compatibility with bioframe/core/construction.py", line 150

  #462 opened a year ago by haleybianchi
  5

• snippers: order of "select" and "snip" matters, but should it

  #502 opened 9 months ago by sergpolly
  0

• Error Running compute-saddle CLI

  #494 opened 10 months ago by GregZs
  8

• Needs a "cool" logo

  #490 opened 10 months ago by thomas-reimonn
  0

• systematic treatment of floating point warnings from numpy

  #482 opened 10 months ago by sergpolly
  0

• Bugs in decay curve tutorial

  #470 opened 10 months ago by bskubi
  1

• snipping.pileup_legacy, 'cooltools.api.snipping' has no attribute 'pileup_legacy'

  #476 opened 10 months ago by Muchmorepig
  1

• Adaptive coarsegraining doesn't work with NumPy 1.24 and later

  #472 opened a year ago by gschuette
  2

• Unable to install with poetry

  #467 opened a year ago by thomas-reimonn
  5

• KeyError: "Column(s) ['balanced.sum'] do not exist"

  #465 opened a year ago by KunFang93
  4

• Error: No such command 'dump-cworld'.

  #463 opened a year ago by songxh1996
  1

• Unable to install cooltools on Windows

  #460 opened a year ago by Devalock
  3

• Downsampling and cis counts

  #458 opened a year ago by ddepierre
  2

• How to visualise .cool files instead of .mcool

  #457 opened a year ago by redjay8
  2

• Balance = True flags an error

  #461 opened a year ago by ratheraarif
  7

• Issue plotting a/b compartment eigs_cis

  #455 opened a year ago by katecycho
  0